Based on the control equations which describe the dynamics of three dimensional compressible atmosphere and the MPI (Message Passing Interface) and the idea of domain decomposition, a parallel numerical model is developed in this paper. The model is used to simulate the gravity waves propagation in three-dimensional compressible atmosphere. Firstly, on the basis of domain decomposition in the vertical direction and the characteristics of the staggered grid system, the main grid lines for vertical velocity are regarded as the lower boundary of the child domain, and the main grid lines for the state variables are regarded as the upper boundary of the child domain. Then, the data communication from one child domain to another is completed by MPI. As a result, the parallel computation on the whole computational domain can be completed successfully. Finally, according to the linear theory for small amplitude gravity waves, we simulated the small amplitude gravity waves propagation and the results indicated that, the propagation of small amplitude gravity wave in three-dimensional atmosphere can be simulated well by our model. The amplitude of gravity wave is increased in the form of exponential with its propagation height increased. The simulated results about the energy path, the available perturbative potential energy and the perturbative kinetic energy are well consistent with the gravity wave's linear theory. Additionally, with the number of processes increasing, the computational time decreases dramatically. All of these indicated that, the parallel numerical model developed in this paper not only can simulate the propagation of gravity waves very well, but also the model can save the computational coast effectively.